In navigation, Heading is the direction the bow is pointing - the helmsman will attempt to maintain that based on his compass. Be advised that a VERY good helmsman will still stray 3-5 degrees at best from that depending on sea state, etc. The actual course made over the ground will vary from that based on wind, current and sea state.
I agree that the use of waypoints simulates the entire chain of the Helmsman, Officer of the Deck and the Navigator all inputting their functions into the maintaining of a plotted course. However, once you are on manual it SHOULD vary based on all the above - but as also been stated it would take a lot of CPU cycles and code to do anything like a good job at simulating ALL the effects.
Just as a case in point - the helmsman was maintaining his plotted course, but the navigator didn't correctly factor in a current - and the result was seven US destroyers out of action. See
http://www.pointhondamemorial.org/.